public interface IReaction extends IChemObject
The class mostly represents abstract reactions, such as 2D diagrams, and is not intended to represent reaction trajectories. Such can better be represented with a ChemSequence.
Modifier and Type | Interface and Description |
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static class |
IReaction.Direction
Permissible reaction directions.
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Modifier and Type | Method and Description |
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void |
addAgent(IMolecule agent)
Adds an agent to this reaction.
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void |
addMapping(IMapping mapping)
Adds a mapping between the reactant and product side to this
Reaction.
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void |
addProduct(IMolecule product)
Adds a product to this reaction.
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void |
addProduct(IMolecule product,
Double coefficient)
Adds a product to this reaction.
|
void |
addReactant(IMolecule reactant)
Adds a reactant to this reaction.
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void |
addReactant(IMolecule reactant,
Double coefficient)
Adds a reactant to this reaction with a stoichiometry coefficient.
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IMoleculeSet |
getAgents()
Returns a IMoleculeSet containing the agents in this reaction.
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IReaction.Direction |
getDirection()
Returns the
IReaction.Direction of the reaction. |
IMapping |
getMapping(int pos)
Retrieves a mapping between the reactant and product side to this
Reaction.
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int |
getMappingCount()
Get the number of mappings between the reactant and product side to this
Reaction.
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Double |
getProductCoefficient(IMolecule product)
Returns the stoichiometry coefficient of the given product.
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Double[] |
getProductCoefficients()
Returns an array of double with the stoichiometric coefficients
of the products.
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int |
getProductCount()
Returns the number of products in this reaction.
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IMoleculeSet |
getProducts()
Returns a IMoleculeSet containing the products of this reaction.
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Double |
getReactantCoefficient(IMolecule reactant)
Returns the stoichiometry coefficient of the given reactant.
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Double[] |
getReactantCoefficients()
Returns an array of double with the stoichiometric coefficients
of the reactants.
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int |
getReactantCount()
Returns the number of reactants in this reaction.
|
IMoleculeSet |
getReactants()
Returns a IMoleculeSet containing the reactants in this reaction.
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Iterable<IMapping> |
mappings()
Returns the mappings between the reactant and the product side.
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void |
removeMapping(int pos)
Removes a mapping between the reactant and product side to this
Reaction.
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void |
setDirection(IReaction.Direction direction)
Sets the direction of the reaction.
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boolean |
setProductCoefficient(IMolecule product,
Double coefficient)
Sets the coefficient of a a product to a given value.
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boolean |
setProductCoefficients(Double[] coefficients)
Sets the coefficient of the products.
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void |
setProducts(IMoleculeSet products)
Assigns a IMoleculeSet to the products of this reaction.
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boolean |
setReactantCoefficient(IMolecule reactant,
Double coefficient)
Sets the coefficient of a a reactant to a given value.
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boolean |
setReactantCoefficients(Double[] coefficients)
Sets the coefficients of the reactants.
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void |
setReactants(IMoleculeSet reactants)
Assigns a IMoleculeSet to the reactants in this reaction.
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addListener, clone, getFlag, getFlags, getID, getListenerCount, getNotification, getProperties, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, toString
getBuilder
int getReactantCount()
int getProductCount()
IMoleculeSet getReactants()
setReactants(org.openscience.cdk.interfaces.IMoleculeSet)
void setReactants(IMoleculeSet reactants)
reactants
- The new set of reactantsgetReactants()
IMoleculeSet getProducts()
setProducts(org.openscience.cdk.interfaces.IMoleculeSet)
void setProducts(IMoleculeSet products)
products
- The new set of productsgetProducts()
IMoleculeSet getAgents()
addAgent(org.openscience.cdk.interfaces.IMolecule)
Iterable<IMapping> mappings()
Iterable
to the Mappings.addMapping(org.openscience.cdk.interfaces.IMapping)
void addReactant(IMolecule reactant)
reactant
- Molecule added as reactant to this reactiongetReactants()
void addAgent(IMolecule agent)
agent
- Molecule added as agent to this reactiongetAgents()
void addReactant(IMolecule reactant, Double coefficient)
reactant
- Molecule added as reactant to this reactioncoefficient
- Stoichiometry coefficient for this moleculegetReactants()
void addProduct(IMolecule product)
product
- Molecule added as product to this reactiongetProducts()
void addProduct(IMolecule product, Double coefficient)
product
- Molecule added as product to this reactioncoefficient
- Stoichiometry coefficient for this moleculegetProducts()
Double getReactantCoefficient(IMolecule reactant)
reactant
- Reactant for which the coefficient is returned.setReactantCoefficient(org.openscience.cdk.interfaces.IMolecule, java.lang.Double)
Double getProductCoefficient(IMolecule product)
product
- Product for which the coefficient is returned.setProductCoefficient(org.openscience.cdk.interfaces.IMolecule, java.lang.Double)
boolean setReactantCoefficient(IMolecule reactant, Double coefficient)
reactant
- Reactant for which the coefficient is setcoefficient
- The new coefficient for the given reactantgetReactantCoefficient(org.openscience.cdk.interfaces.IMolecule)
boolean setProductCoefficient(IMolecule product, Double coefficient)
product
- Product for which the coefficient is setcoefficient
- The new coefficient for the given productgetProductCoefficient(org.openscience.cdk.interfaces.IMolecule)
Double[] getReactantCoefficients()
setReactantCoefficients(java.lang.Double[])
Double[] getProductCoefficients()
setProductCoefficients(java.lang.Double[])
boolean setReactantCoefficients(Double[] coefficients)
coefficients
- An array of double's containing the coefficients of the reactantsgetReactantCoefficients()
boolean setProductCoefficients(Double[] coefficients)
coefficients
- An array of double's containing the coefficients of the productsgetProductCoefficients()
void setDirection(IReaction.Direction direction)
direction
- The new reaction directiongetDirection()
IReaction.Direction getDirection()
IReaction.Direction
of the reaction.setDirection(Direction)
void addMapping(IMapping mapping)
mapping
- Mapping to add.mappings()
void removeMapping(int pos)
pos
- Position of the Mapping to remove.mappings()
IMapping getMapping(int pos)
pos
- Position of Mapping to get.int getMappingCount()